Salmonella serotyping is shifting from slide agglutination toward whole-genome sequencing (WGS). While WGS allows for comprehensive analyses, phenotypic information about lipopolysaccharide-deficient ("LPS-rough") isolates obtained from slide agglutination is lost. This discrepancy represents a challenge for Salmonella control in livestock because in the European Union, LPS-rough Salmonella isolated from food-producing animals that are untypable using slide agglutination alone are not subject to control measures, whereas isolates of certain serovars in certain matrices would be, when based on geno-serotyping. Here, we provide an account of the relevance of this phenotype in the context of routine diagnostics and food safety by characterizing the occurrence, diversity, and isolation matrices of LPS-rough isolates among non-human Salmonella enterica subsp. enterica isolates from Germany. Using available WGS data, we examined phylogenetic relationships and associations with certain genomic features. On average, 5% of isolates exhibited an LPS-rough phenotype across 46 serovars, but clonal distribution of this phenotype along the food chain was not evident. LPS-rough isolates were more commonly found in S. Choleraesuis isolated from wild boar and in S. Typhimurium isolated from pork products, compared with other matrices. We also found associations with two virulence factors, an AMR gene, and a plasmid marker. The present work lays the foundation for future research into the role of certain matrices, environments, or genomic factors in the development of LPS-rough Salmonella isolates and will facilitate the elucidation of the genomic basis of this phenotype, which may improve recommendations regarding risk management and control measures.IMPORTANCEThe present work highlights some of the challenges associated with the recent shift from serology- to sequence-based typing of Salmonella enterica serovars and provides a national perspective on the presence and relevance of the lipopolysaccharide-deficient ("LPS-rough") phenotype in samples obtained from food, animals, and the environment, including considerations regarding the choice of typing method. We provide evidence that clonal distribution of isolates with this phenotype is unlikely, but that certain environments may favor its development, and certain genomic factors may increase survival rates of LPS-rough isolates when exposed to environmental stressors. These findings could have important implications for regulations regarding the surveillance and management of Salmonella isolated from food, feed, and animals in the future, in particular in the context of using different typing methods, and warrant further detailed research.

HLA-DPB1*04:02:34 differs from HLA-DPB1*04:02:01:01 by one nucleotide substitution in codon 49 in exon 2.

HLA-DPB1*04:01:97 differs from HLA-DPB1*04:01:01:04 by one nucleotide substitution in codon 123 in exon 3.

HLA-A*11:217 differs from HLA-A*11:01:01:01 by one nucleotide substitution in codon 21 in exon 2.

HLA-DRB1*04:395 differs from HLA-DRB1*04:05:01:05 by one nucleotide substitution in codon 104 in exon 3.

HLA-C*07:1189 differs from HLA-C*07:04:01:01 by one nucleotide substitution in codon 211 in exon 4.

Bovine leukemia virus (BLV), the most prevalent neoplastic disease of cattle worldwide, is the causative agent of enzootic bovine leukosis. Polymorphisms in the bovine leukocyte antigen (BoLA)-DRB3 gene can influence host immune responses to pathogens, including BLV. However, the associations between specific BoLA-DRB3 alleles, BLV proviral load (PVL), a useful index for estimating disease progression and transmission risk, and BLV infection in Chinese cattle remain unknown. In this study, we identified 28 previously reported alleles in 289 Holstein cattle from Shandong Province, China, using polymerase chain reaction sequence-based typing. We further investigated whether BoLA-DRB3 polymorphisms influenced infection status and identified BoLA-DRB3*011:01 as an allele associated with susceptibility to BLV infection. An association analysis of allele frequencies between cattle with high and low PVL demonstrated that BoLA-DRB3*014:01:01 was significantly associated with low PVL. Farms with a higher frequency of cattle carrying BoLA-DRB3*014:01:01 had lower mean PVL values than farms with a lower frequency, indicating that resistant alleles are linked to low PVL levels. To our knowledge, this is the first study to demonstrate that BoLA-DRB3 polymorphisms associate with differential susceptibility to BLV infection and PVL in Holstein cattle in China. These findings may contribute to BLV control and eradication efforts through genetic selection.

Clostridium butyricum has been identified in fecal samples from both asymptomatic neonates and cases of necrotizing enterocolitis (NEC). Using a large collection of strains from different origins and spatiotemporal contexts, we developed and established a cgMLST scheme for the molecular typing of C. butyricum. Our results show that most C. butyricum strains cluster independently of origin and spatiotemporal context factors. However, specific cgMLST clades of C. butyricum were found for plant and botulinum neurotoxin type E strains. Clonal strains were also identified. No specific cgMLST clade was found to be genetically associated with NEC. cgSNP showed higher discriminatory power compared to cgMLST. Importantly, cgSNP provided better discriminatory power for strain relatedness with respect to strains isolated from NEC patients.

The D--phenotype is an extremely rare RhCE variant characterized by the complete absence of RhCE antigens in the Rh blood group system and is associated with a highly complex molecular mechanism. In this study, several D--individuals with discrepancies between phenotypic and genotypic results were analyzed, and a complex RH gene inversion-recombination variant with a novel breakpoint was identified via multi-platform analyses. Six D--individuals from the Chinese population were collected. The full-length sequences of the RHD, RHCE, and RHAG genes were amplified, and long-read haplotype sequencing was performed using PacBio technology. Complex structural variations in the RH gene were detected through Bionano Optical Genome Mapping (OGM). Lastly, fusion regions in the RHCE haplotype were amplified and sequenced using PacBio technology and PCR-SBT. PacBio third-generation haplotype sequencing (TGS) suggested the presence of potential structural variants. Subsequently, Bionano optical genome mapping (OGM) identified a complex gene inversion and recombination structural variant, designated RHCE*Ce(1-2)-D(3-10)-TMEM50A-Ce(10-8)-Ce(3-10). Moreover, a novel fusion breakpoint was validated by PacBio haplotype sequencing and PCR sequencing-based typing (PCR-SBT). The structural inversion, which originated within intron 7 of the RHCE gene at chr1: 25377650, was rejoined to intron 2 at chr1: 25404500, forming a novel breakpoint. Finally, all D--individuals in this study harbored this complex structural variation with an identical breakpoint position. The RH gene inversion and recombination may represent a prevalent molecular basis for the D--phenotype in the Chinese population. These findings expand our understanding of the molecular mechanisms underlying the Rh blood group system and hold significant implications for transfusion safety in individuals with this rare D--phenotype.

A large outbreak investigation of Legionnaires' disease associated with a public bath facility in Hiroshima, Japan, using PFGE, SBT, MLVA, and whole-genome sequencing.

HLA-A*02:558 differs from HLA-A*02:06:01:01 by one nucleotide substitution in codon 96 in exon 3.

HLA-DPB1*1784:01 differs from HLA-DPB1*514:01 by one nucleotide substitution in codon 57 in exon 2.

BackgroundThe gold standard for detecting HLA-B*57:01 allele linked to Abacavir hypersensitivity is sequence-based typing (SBT), which is labour-intensive, not readily available and needs special expertise. HCP5 gene polymorphism is a surrogate marker for HLA-B*57:01 allele. Therefore, we compared, nested PCR for HLA-B*57:01 allele, HCP5 PCR with SBT method to develop a simple and cost-effective method for detection of HLA-B*57:01 allele.MethodWhole blood cells were collected from PLHIV and Buffy coat and DNA was isolated. Direct PCR for HLA-B*57 gene followed by nested PCR for the HLA-B* 57:01 allele and HCP5 gene PCR was done in all patients. The PCR results of both methods were confirmed by the SBT method.ResultAmong 366 samples, 25 (6.83%) were positive for HLA-B* 57:01 allele by nested PCR. HCP5 gene PCR was positive in 25 (6.83%) individuals who were also positive for the HLA-B*57:01 allele with nested PCR. A strong correlation was observed between the HLA-B*57:01 allele and HCP5 with negative and positive predictive values of 100% respectively in our population.ConclusionNested (two-step) and HCP5 gene PCR (single-step) are simple, rapid and cost-effective methods for HLA-B*57:01 allele detection and either can be adapted in the ART centre located in resource-poor settings.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12879-025-11790-w.

HLA-C*03:703 differs from HLA-C*03:620 by one nucleotide substitution in codon 114 in exon 3.

BackgroundNodding syndrome (NS) is a disabling childhood-onset epilepsy occurring in onchocerciasis-endemic regions. High Onchocerca volvulus microfilarial loads in childhood are a key risk factor, but not all heavily infected individuals develop NS, suggesting a possible role for host genetic susceptibility. Human leukocyte antigen (HLA) haplotypes have been implicated in susceptibility to various infectious and autoimmune diseases, including onchocerciasis. We investigated potential associations between HLA haplotypes and onchocerciasis-associated epilepsy (OAE), including NS, in Tanzania.MethodsA case-control study was conducted in an onchocerciasis-endemic area in the Mahenge area, Tanzania, including 98 persons with epilepsy and 112 controls. DNA was extracted from dry blood spots and HLA sequence-based typing was performed by Histogenetics (Ossining, USA). A total of 11 HLA loci (HLA-A, -B, -C, -DRB1, -DRB3, -DRB4, -DRB5, -DQA1, -DQB1, -DPA1, and -DPB1) were exon sequenced. The HLA-typed dataset was analysed using pyHLA, including Bonferroni as multi-test adjustment, to test for associations with O. volvulus anti-Ov16 seropositivity, epilepsy, OAE and NS.ResultsAnti-Ov16 seropositivity was significantly higher in cases than controls (76.5% vs 58.9%; p = 0.01). No HLA alleles were significantly associated with epilepsy, OAE, NS, or anti-Ov16 seropositivity after correction. Before adjustment, HLA-C07:01 appeared to be a risk factor for epilepsy, HLA-DQB106:02 was associated with OAE, HLA-B35:01 with NS, and HLA-C08:02 and DRB1*03:01 with anti-Ov16 seropositivity. Post-hoc power analysis indicated that substantially larger sample sizes would be required to confirm these associations.ConclusionsThis study did not identify statistically significant HLA associations with epilepsy, OAE, NS, or O. volvulus exposure. However, several alleles—particularly HLA-B*35:01, also reported in a previous South Sudanese study—emerged as potential candidates for further investigation. Larger, multi-country studies with sufficient power are needed to clarify whether host genetic factors contribute to susceptibility to OAE and NS. Strengthening onchocerciasis elimination programmes remains essential, as NS is a preventable disease.

HLA-B*35:433 was fully characterised using sequence-based typing after haplo-specific amplification.

HLA-B*39:194Q differs from HLA-B*39:01:01:03 by a single nucleotide substitution in codon -24.

HLA-B*27:05:64 differs from HLA-B*27:05:02:05 by one nucleotide substitution in codon -21 in exon 1.

HLA-B*44:357:02 differs from HLA-B*44:357:01 by one nucleotide substitution in codon 160 in exon 3.

HLA-C*07:1184 differs from HLA-C*07:01:01:01 by one nucleotide substitution in codon-18 in exon 1.